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- PDB-2pcu: Human carboxypeptidase A4 in complex with a cleaved hexapeptide. -

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Basic information

Entry
Database: PDB / ID: 2pcu
TitleHuman carboxypeptidase A4 in complex with a cleaved hexapeptide.
Components
  • Carboxypeptidase A4
  • peptide
KeywordsHYDROLASE / metallocarboxypeptidase / metalloprotease / product / cleavage / specificity / human carboxypeptidase A4
Function / homology
Function and homology information


hormone catabolic process / peptide catabolic process / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / metallocarboxypeptidase activity / proteolysis / extracellular space / zinc ion binding
Similarity search - Function
Carboxypeptidase A, carboxypeptidase domain / Carboxypeptidase, activation peptide / Metallocarboxypeptidase-like, propeptide / Carboxypeptidase activation peptide / Zinc carboxypeptidases, zinc-binding region 2 signature. / Zinc carboxypeptidases, zinc-binding region 1 signature. / Peptidase family M14 domain profile. / Zn_pept / Peptidase M14, carboxypeptidase A / Zinc carboxypeptidase ...Carboxypeptidase A, carboxypeptidase domain / Carboxypeptidase, activation peptide / Metallocarboxypeptidase-like, propeptide / Carboxypeptidase activation peptide / Zinc carboxypeptidases, zinc-binding region 2 signature. / Zinc carboxypeptidases, zinc-binding region 1 signature. / Peptidase family M14 domain profile. / Zn_pept / Peptidase M14, carboxypeptidase A / Zinc carboxypeptidase / Zn peptidases / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ASPARTIC ACID / THIOCYANATE ION / Carboxypeptidase A4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBayes, A. / Fernandez, D. / Sola, M. / Marrero, A. / Garcia-Pique, S. / Aviles, F.X. / Vendrell, J. / Gomis-Ruth, F.X.
CitationJournal: Biochemistry / Year: 2007
Title: Caught after the Act: a human A-type metallocarboxypeptidase in a product complex with a cleaved hexapeptide.
Authors: Bayes, A. / Fernandez, D. / Sola, M. / Marrero, A. / Garcia-Pique, S. / Aviles, F.X. / Vendrell, J. / Gomis-Ruth, F.X.
History
DepositionMar 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carboxypeptidase A4
B: peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4307
Polymers34,8602
Non-polymers5705
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-38 kcal/mol
Surface area12370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.304, 72.494, 81.575
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide / Sugars , 3 types, 3 molecules AB

#1: Protein Carboxypeptidase A4 / Carboxypeptidase A3


Mass: 34227.398 Da / Num. of mol.: 1 / Fragment: Carboxypeptidase A4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CPA4, CPA3 / Production host: Pichia pastoris (fungus)
References: UniProt: Q9UI42, Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases
#2: Protein/peptide peptide


Mass: 632.731 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesised
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 271 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7NO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Crystals were obtained from sitting drops subjected to vapor diffusion and containing consisting of 100nL of hCPA4:hexapeptide (15 mg/mL in 5mM Tris HCl pH 7.5) and 100nL of reservoir ...Details: Crystals were obtained from sitting drops subjected to vapor diffusion and containing consisting of 100nL of hCPA4:hexapeptide (15 mg/mL in 5mM Tris HCl pH 7.5) and 100nL of reservoir solution (0.2M potassium thiocyanate / 20% PEG 3350). Crystallisation drops were dispensed on 96x3-well Greiner plates by a Tecan robot and a Cartesian nanodrop robot (Genomic Solutions) at the joint IBMB-CSIC/Barcelona Science Park Automated Crystallization Platform (PAC). Crystals appeared after incubation for 10-15 days in a Bruker steady-temperature crystal farm at 4 C., VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.036 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 1, 2006
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.036 Å / Relative weight: 1
ReflectionResolution: 1.6→72.548 Å / Num. obs: 39536 / % possible obs: 98.7 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 4.1
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 2 / Num. measured all: 17578 / Num. unique all: 5427 / Rsym value: 0.346 / % possible all: 95.1

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
ProDCdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BO9

2bo9


Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.967 / SU B: 3.252 / SU ML: 0.052 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.176 609 1.5 %RANDOM
Rwork0.159 ---
all0.159 39536 --
obs0.159 39478 98.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.621 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å20 Å20 Å2
2---1.29 Å20 Å2
3---2.23 Å2
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2461 0 33 267 2761
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222589
X-RAY DIFFRACTIONr_angle_refined_deg1.6261.9423517
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9955308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.51723.413126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.4515408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2191518
X-RAY DIFFRACTIONr_chiral_restr0.120.2375
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022002
X-RAY DIFFRACTIONr_nbd_refined0.2210.21294
X-RAY DIFFRACTIONr_nbtor_refined0.3210.21781
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2223
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3450.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1270.223
X-RAY DIFFRACTIONr_mcbond_it1.0941.51562
X-RAY DIFFRACTIONr_mcangle_it1.70722521
X-RAY DIFFRACTIONr_scbond_it2.66931027
X-RAY DIFFRACTIONr_scangle_it4.1384.5996
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 38 -
Rwork0.18 2596 -
obs-2634 90.67 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.811-0.26030.09621.28770.41320.82060.026-0.01490.08810.0006-0.0424-0.1055-0.01730.00090.0164-0.1046-0.00460.0004-0.0851-0.0115-0.11661.517631.667611.6948
20.94-0.28290.03021.4490.41780.80960.0269-0.00340.08420.0108-0.0299-0.1075-0.0013-0.00760.003-0.0889-0.0047-0.0071-0.0648-0.0108-0.10441.43931.623711.3951
30.67582.7941-0.267314.66752.69344.73890.1182-0.0653-0.18210.0323-0.024-0.1620.1748-0.0543-0.0942-0.00030.0119-0.02040.0566-0.04470.01040.558745.177421.4697
41.2293-0.2596-0.08621.62570.30460.80090.0251-0.00540.0684-0.0273-0.0451-0.0941-0.0282-0.00140.020.0257-0.0118-0.00450.072-0.0005-0.00971.513832.046211.2844
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 308
2X-RAY DIFFRACTION2A901
3X-RAY DIFFRACTION2A999
4X-RAY DIFFRACTION3B1 - 5
5X-RAY DIFFRACTION4A501 - 502

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